Erik Kusch

Senior Engineer

Machine Readable Nature Research Group (MANA)

Department of Research and Collections

Natural History Museum

University of Oslo

Erik Kusch

GLOBAL BIODIVERSITY

INFORMATION

FACILITY

GBIF –Occurrence Data for Your Research

Erik Kusch

What is GBIF?

Erik Kusch

Intergovernmental network and

research infrastructure

Provides anyone, anywhere, free and

open access to data about all types of

life on Earth

Voluntary collaboration through

Memorandum of Understanding

(MoU)

Participant nodes, Secretariat in

Copenhagen, Denmark

What is GBIF?

Erik Kusch

4BY THE NUMBERS | 14th November 2023

Country

Participants 44

Organization

Participants 9 532

Peer-review papers

using data

2 615 608 802

Species occurrence records 91 030

Datasets

2 643

Publishers

>119 billion

Records downloaded per month in 2022

Erik Kusch

5BY THE NUMBERS | 14th November 2023

Country

Participants 44

Organization

Participants 9 532

Peer-review papers

using data

2 615 608 802

Species occurrence records 91 030

Datasets

2 643

Publishers

>119 billion

Records downloaded per month in 2022

Erik Kusch

6Data From the GBIF Network | 14th November 2023

Erik Kusch

7BY THE NUMBERS | 14th November 2023

Country

Participants 44

Organization

Participants 9 532

Peer-review papers

using data

2 615 608 802

Species occurrence records 91 030

Datasets

2 643

Publishers

>119 billion

Records downloaded per month in 2022

Erik Kusch

8Data Sets in GBIF

Erik Kusch

9BY THE NUMBERS | 14th November 2023

Country

Participants 44

Organization

Participants 9 532

Peer-review papers

using data

2 615 608 802

Species occurrence records 91 030

Datasets

2 643

Publishers

>119 billion

Records downloaded per month in 2022

Erik Kusch

10 Data From the GBIF Network | 14th November 2023

Map updated 2023-11-14

https://www.gbif.org/the-gbif-network

Erik Kusch

11 BY THE NUMBERS | 14th November 2023 - Norway

235

Peer-review papers

using data (co-author

from Norway

49 347 021

Species occurrence records

(published from)

426

Datasets

(published from)

Publishers

(from Norway)

Erik Kusch

What Data is in GBIF?

Erik Kusch

13 Evidence About Where Species HAVE Lived & When

Digitized

specimens

Observations

Literature

Remote-sensing Environmental

DNA

Common

standards

(DwC)

Data publishing

and indexing

Data discovery and use

Erik Kusch

14 Data Models in GBIF

Data richness levels

supported by Gbif

Dataset description,

taxonomic/geographic/temporal scope

Dataset metadata

List of taxa

regional or thematic (e.g. invasive, medicinal)

Species checklists

Species occurrences and sampling events

dates, coordinates, sampling effort / protocol,

abundance

Sampling-event data

Species occurrences

dates, coordinates, basis of record

Occurrence-only data

Erik Kusch

15 Sources of GBIF Data: Digitized Museum Collections

Erik Kusch

16 Sources of GBIF Data: Taxonomic Literature

Data

liberation

Erik Kusch

17 Sources of GBIF Data: DNA Derived Occurrences

Erik Kusch

18 Sources of GBIF Data: Peer-Reviewed Publications

Erik Kusch

19 Sources of GBIF Data: Citizen Science Observations

Erik Kusch

Using GBIF Data

Erik Kusch

21 GBIF: Multiple-Purpose Data Publishing Services

Research

data portals

portal

Bio-Collections

& ecology datasets

Environment

directive

reporting

Erik Kusch

22 Supporting Research and Sustainable Development

Conservation

- Protected areas

- Threatened species

- Invasive species risk

Food Security

- Crop wild relatives

In situ

ex situ

conservation

of genetic diversity

- Fisheries planning

Climate change

- Modelling impacts on

species ranges

- Adaptation strategies

- Mitigation benefits, risks

Human health

- Disease risk based on

occurrence of vectors, hosts,

reservoirs

- Medicinal plants

- Hazards e.g. snakebite

Erik Kusch

23 Biodiversity Evidence for Research and Policy

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GBIF Data Considerations

Erik Kusch

25 Taxonomic Biases

Image: FL Fawcett in Wheller Ann. Entomol. Soc. Am. 1990

Troudet et al. Nature Scientific Reports 2017

1200 mill.

animals

300 m

plants

20 m

fungi

16 m

bacteria 0,04 m

virus

Erik Kusch

26 Spatial Bias

Observations are:

where people go

driven by visibility

Erik Kusch

27 Temporal Bias

1832-18372017-2022

Erik Kusch

28 Data Issues and Flags

Suite of flags for determining data

quality

The ones to look for especially

Taxon match fuzzy

Taxon match higherrank

Coordinate rounded

Coordinate uncertainty in metres

! 0;0 !

Erik Kusch

29 (Art and Science) of Taxonomy

Taxonomic homonyms: when filtering based on scientific name, check if all the results are in the same part of taxonomic tree

(at least kingdom)

Cuspidaria cuspidata (Olivi, 1792) Cuspidaria cuspidata (M. Bieb.) Takht.

Erik Kusch

30 Data Size

The size of the dataset you download can be substantial, depending

on the extent of your query. Ensure you have the necessary storage and

computational resources to handle the data.

Consider using BigQuerry or Apache Spark for interactions with really

big data.

Only query what you need.

Erik Kusch

Accessing GBIF Data

Erik Kusch

32 BY THE NUMBERS | 14th November 2023

Country

Participants 44

Organization

Participants 9 532

Peer-review papers

using data

2 615 608 802

Species occurrence records 91 030

Datasets

2 643

Publishers

>119 billion

Records downloaded per month in 2022

Erik Kusch

33 How are Data Indexed in GBIF?

GBIF translates traditional nomenclature into Operational Taxonomic Units

(OTUs)

PhyloCode

Domain (Eukarya)

Phylum (Chordata)

Order (Primates)

Genus (Homo)

Species (Homo sapiens)

Family (Hominidae)

Class (Mammalia)

Kingdom (Animalia)

Erik Kusch

34 OTUs and the GBIF Backbone

Species Hypothesis (SH) numbers [DOI]

BIN DEF0002SH ABC0001

GBIF

backbone

taxonomy Barcode Identification Number (BIN)

Erik Kusch

35 Machine-Readability Requires Persistent Identifiers

The purpose of identifiers is

… to name things

… making it possible to refer to them

To uniquely identify something it needs a persistent identifier, a PID.

A Persistent Identifier is globally unique,persistent, and resolvable“.

A PID is resolvable when it allows both human and machine users to access an object or its representation, and its

Kernel

Information.

Kernel Information is a structured record that contains information (metadata) about the referred object, such as a pointer to the location where the data for the object can be

found.

Erik Kusch

FAIR data is about

machine-readable

data

researchers & museums need to do more than simply post their data on the web for it to be re-usable.

Erik Kusch

37 GBIF & Identifiers

https://www.gbif.org/occurrence/1095052193

Dataset

: Vascular Plant

Herbarium, Oslo (O) UiO

Publisher

: University of Oslo

Catalogue number

: 2007334

Erik Kusch

•GBIF trawling for data via GBIF

Data Portal

•Search can be refined via filters Dataset

metadata

Species

checklists

Sampling-

event data

Occurrence

data

Discovering Data in GBIF –The Data Portal

Erik Kusch

Download through the GBIF Data Portal is a three-step process:

1. Select desired data

2. Stage download & wait for GBIF to finish processing

3. Download final product

Downloading Data in GBIF –The Data Portal

Erik Kusch

Discovery & Download takes four R function calls:

1. Initial Data Search: occ_search(…)

2. Asynchronous download:

1. occ_download(…)

2. occ_download_get(…)

3. occ_download_import(…)

Programmatic Data Discovery & Download

occ_initial

Erik Kusch

41 Long-Term Download Accessibility

We store all download files as long as

possible.

The download metadata page will always

resolve, but the file itself might be

removed in the future.

We strive to store all downloads, but

prioritize downloads that have been cited.

Erik Kusch

Accrediting GBIF Data

Erik Kusch

43 BY THE NUMBERS | 14th November 2023

Country

Participants 44

Organization

Participants 9 532

Peer-review papers

using data

2 615 608 802

Species occurrence records 91 030

Datasets

2 643

Publishers

>119 billion

Records downloaded per month in 2022

Erik Kusch

44 How to Cite Data Mediated by GBIF

1. Download data from GBIF.org

2. and receive recommended citation with a download DOI

3. Cite the DOI in published research or other work

Example

: GBIF.org (9 November 2021) GBIF Occurrence Download https//doi.org/10.15468/dl.xxxxxx

Erik Kusch

45 Downloads and Datasets are Assigned DOIs

Citing the data download DOI will resolve to the dataset DOIs assigned for each dataset

contributing data records to the download set.

This way, all data publishers contributing data records will be accredited!

Erik Kusch

Source dataset #1

Source dataset #2

Source dataset #3

GBIF download

Publish

datasets

in GBIF

Final state of data

Dataset DOIs Download DOI Bibliographic DOI

Analyze

& publish

Process &